NOTE:
ips
contains most functions that were formerly included in thephyloch
package plus some more recent functions. Thosephyloch
functions related to tree plotting have been moved to theviper
package.
This is a bundle of functions that present interfaces to popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states. In additions, there functions for reading, manipulating and writing phylogenetic data (multiple sequence alignments and phylogenetic trees).
There are several functions for reading and writing DNA sequences in
FASTA, PHYLIP, and NEXUS format: read.fas
,
read.phy
, read.nex
, write.fas
,
write.phy
, and write.nex
. Some functions are
available for integrating BEAST with R. XML input files for BEAST can be
generated with rbeauti
. Two functions are designed to read
TreeAnnotator output: read.beast
will render an object of
class phylo
with additional node statistics appended as
list elements. These additional node statistics will be lost be the
subsequent use of ladderize
or rotate
(or
similar functions that change the ordering of internal
nodes).read.beast.table
also parses the TreeAnnotator
output, but returns a matrix of node statistics. This package itself
does not implement techniques for phylogenetic analyses, but provides a
series of wrappers for commonly used software packages. Sequence
alignment can be done with the mafft
and
prank
; cleaning of sequences with gblocks
and
aliscore
. The function raxml
and
mrbayes
are intended for phylogentic tree search. Running
mrbayes
with argument run = FALSE
can be used
to create MrBayes-executable NEXUS files. Finally, wrappers are provided
for Multistate
in the BayesTraits
package (see
multistateML
and multistateMCMC
). Several
plotting functions (HPDbars
, clade.bars
,
box.clades
, box.tips
, tip.color
,
edge.color
have been moved to the viper
package.
ips
is available via CRAN and can be installed:
install.packages("ips")
Or you can install the development version via GitHub with:
# install.packages("devtools")
::install_github("heibl/ips") devtools